Variant report

Variant	rs2126635
Chromosome Location	chr4:22434907-22434908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22433445..22435816-chr4:22516699..22518877,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152990	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10938897	0.89[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10938898	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10938899	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11935142	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11940612	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12503615	0.83[JPT][hapmap]
rs13109695	0.89[CEU][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13135121	0.89[CEU][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13140185	0.89[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13140367	0.89[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1462995	0.89[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1462996	0.88[CEU][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1462997	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs1463000	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs1564135	0.89[CEU][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1564136	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1841824	0.84[CEU][hapmap];0.82[MKK][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1841825	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1841826	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1841827	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1841828	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1947738	0.89[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4627850	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4697305	0.83[JPT][hapmap]
rs59602170	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6448155	0.89[CEU][hapmap]
rs6830873	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6831918	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6853811	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6854785	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855127	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3451628	chr4:22432848-22435807	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2126635	LGI2	cis	cerebellum	SCAN
rs2126635	GPR125	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22371600-22449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:22383200-22438000	Weak transcription	Lung	lung
3	chr4:22383600-22442800	Weak transcription	A549	lung
4	chr4:22386000-22446600	Weak transcription	Fetal Thymus	thymus
5	chr4:22388200-22442800	Weak transcription	Brain Germinal Matrix	brain
6	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
8	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
9	chr4:22390600-22439600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:22390600-22456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:22393000-22435200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:22393400-22444800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:22393800-22446400	Weak transcription	NH-A	brain
16	chr4:22393800-22453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:22399800-22442800	Weak transcription	Fetal Brain Female	brain
18	chr4:22400000-22448000	Weak transcription	Left Ventricle	heart
19	chr4:22400800-22449600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:22400800-22461800	Weak transcription	Gastric	stomach
21	chr4:22405400-22446000	Weak transcription	Pancreas	Pancrea
22	chr4:22412800-22446000	Weak transcription	Thymus	Thymus
23	chr4:22416800-22449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:22417600-22442200	Weak transcription	Hela-S3	cervix
25	chr4:22417800-22436200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:22418000-22435200	Strong transcription	Liver	Liver
27	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
29	chr4:22420200-22436400	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
31	chr4:22420800-22436400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:22421200-22442600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:22422000-22441400	Weak transcription	Right Ventricle	heart
34	chr4:22422000-22453400	Weak transcription	Esophagus	oesophagus
35	chr4:22422600-22442800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:22424400-22457800	Weak transcription	Dnd41	blood
37	chr4:22424600-22448000	Weak transcription	Fetal Kidney	kidney
38	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:22426200-22436800	Weak transcription	HepG2	liver
40	chr4:22426200-22442400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:22426200-22443200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:22426400-22437400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:22426600-22437000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:22426800-22442800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:22427000-22439000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:22427400-22444400	Weak transcription	Primary T cells from cord blood	blood
47	chr4:22427600-22437400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:22427800-22435200	Weak transcription	Fetal Stomach	stomach
49	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
50	chr4:22429200-22443400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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